Large Differentiation of Extremely Threatened Chinese Pangolins Provide New Genomic Cues for Their Conservation

Human-induced poaching and trafficking has a substantial negative impact on the population growth and range expansion of the Chinese pangolin. However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicates a promising sign for the recovery of this threatened species. Therefore, to ascertain population structure and genetic status of this species, we re-sequenced genomes of 15 individuals in Guangdong province and performed a comprehensive population genomics analyses with previously published 21 individuals of Yunnan province. These Chinese pangolins were divided into three distinct populations, with one population consisted of only individuals from Guangdong (CPA), one mixed with Guangdong and Yunnan individuals (CPB) and one Yunnan specific population (CPC). Especially, the CPC population is genetically distinct from the other two population with an extremely large fixation index ( FST ≈ 0.5), which we suggested an independent management unit for future protection and conservation. Further, all these three populations had low genome-wide diversity, high proportion of runs of homozygosity (ROH) in genomes, and a considerable amount of mutation load, which could pose serious threats to the long-term persistence of this species. However, the CPC population showed lower level of genetic load and less long ROH than the other two populations, indicating a potential resource for genetic rescue of other Chinese pangolin populations.